It has long been recognized that certain sites within a protein, such as sites in the protein
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …

The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect
human cells, is the basis for many vaccines and a hotspot of concerning virus evolution …

Adaptation proceeds through the selection of mutations. The distribution of mutant fitness
effect and the forces sha** this distribution are therefore keys to predict the evolutionary …

Influenza is notable for its evolutionary capacity to escape immunity targeting the viral
hemagglutinin. We used deep mutational scanning to examine the extent to which a high …

The influenza virus polymerase is central to influenza virus evolution. Adaptive mutations
within the polymerase are often a prerequisite for efficient spread of novel animal-derived …

Many models of evolution calculate the rate of evolution by multiplying the rate at which new
mutations originate within a population by a probability of fixation. Here we review the …

When detecting positive selection in proteins, the prevalence of errors resulting from
misalignment and the ability of alignment filters to mitigate such errors are not well …

For decades, rates of protein evolution have been interpreted in terms of the vague concept
of functional importance. Slowly evolving proteins or sites within proteins were assumed to …

HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid
sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for …

Functional residues in proteins tend to be highly conserved over evolutionary time.
However, to what extent functional sites impose evolutionary constraints on nearby or even …